Metagenomic analysis of double-stranded DNA viruses in healthy adults
Overview The human body is host to a very large and diverse community of microbial organisms. These organisms may induce illness or disease, but may also aid in staying healthy. The abundance of microbial organisms is very apparent, consisting of bacteria and viruses in virtually all parts of the body. The normal flora of the human body are in places such as the nose, mouth, skin, vagina, and gastrointestinal tract. In this Metagenomic analysis, these body locations were all used to sample the microbiota at each specific location to determine the typical types of viruses in our bodies. The entirety of this study is based on the Human Microbiome Project in which whole-genome shotgun sequencing data was recovered for the microbial community. This data was then taken to perform a thorough analysis of eukaryotic DNA viruses, which could effectively give more insight to the human virome. Interestingly enough, this particular study was "the first large-scale molecular analysis of the viral flora"1. The idea of this study is to identify viruses in asymptomatic adults, meaning that the viruses do not have active pathogenesis. ] The Study This study included 102 people that were used for sampling, half of which had a minimum of 2 samples taken from at least one body location throughout the process of the study. Overall, 706 samples were obtained as data from the following body sites: Nose, mouth, skin, vagina, and stool. Although the design was to analyze double stranded DNA (dsDNA) viruses, single stranded DNA (ssDNA) viruses were also assessed because during replication, ssDNA viruses produce dsDNA intermediates which were detectable because of protocols within the procedure, such as sequencing assays. The human host does contain DNA viruses that are stable components of the human body as well as DNA viruses that are transient in a particular individual. Knowing that''' the virome of a person can change over time', multiple samples (as previously stated) were taken from an individual anywhere from 30 to 359 days apart. Conclusive evidence showed a variety of viral genera within the test subjects, as expected. Results The study showed an average of '''5.5 viral genera per person' and about 92% of the subjects had at least one viral genera obtained through sample. Along with the presence of these viruses in the host, the types of viruses were proven to be consistent with the anatomical location they are typically associated with. There were 7 specific families of human DNA viruses recovered from the samples. The 7 Viral families recovered: # Herpesviridae (dsDNA) #* Includes Human Herpes Viruses such as Roseolovirus (HHV-6,7), HHV-5, Herpes Simplex Virus-1, and Epstein Barr Virus # Papillomaviridae (dsDNA) #* Includes Alpha, beta, and gamma Human Papilloma Virus (HPV) such as HPV-16 and HPV-18 (high risk HPV), ] HPV-19, and HPV-45 # Polyomaviridae (dsDNA) #* Multiple tumor-forming virus; Includes HPyV-6, HPyV-7, and JC virus # Adenoviridae (dsDNA) #* Associated with mouth and skin samples # Anelloviridae (ssDNA) #* All body sites but not in the stool # Parvoviridae (ssDNA) #* Associated with Adenoviridae # Circoviridae (ssDNA) #* Associated with mouth and stool, suggesting it can survive through the GI tract Virus Locations * The Roseolovirus, mostly HHV-7, was found in 98% of people that had samples obtained from the mouth (saliva) ** Proven my multiple samples from the multiple participants * 33% of people had Roseolovirus in the nose (anterior nares) * Alpha-HPV was found in 38% of the people who had vaginal samples * Beta and Gamma HPV was found in 48% of people who had samples obtained from the nose (anterior nares) * Stool samples were minimal, but Roseolovirus and Circovirus were detected Association with Bacteria The likelihood of different viruses to be found in the vagina has been proven to be linked to normal flora. For example, the study showed that Alpha-HPV strains (oncogenic; high-risk) were found in women that had lower counts of Lactobacillus (normal flora of the vagina) and higher counts of anaerobic bacteria. Other relationships were not very apparent in this study, but the idea that bacteria, viruses, and the human host all play a role in creating the particular environment that nurtures life is accepted. Importance of the Metagenomic Analysis Using high-throughput deep metagenomic shotgun sequencing, researchers have been able to identify the human virome and make further conclusions about it. The normal viral flora includes Herpesviridae, Papillomaviridae, Polyomaviridae, Adenoviridae, Anelloviridae, Parvoviridae, and Circoviridae. Although there are many other viruses that have entered the human host, these 7 families can provide a starting point for further research into the effects of each virus. We can study the short term and long term effects as well as the risks of disease that each can impose on humans. Some viruses are not bad because they actually help generate an effective immune response against a pathogenic bacterium. References # Metagenomic analysis of double-stranded DNA viruses in healthy adults (PMCID: PMC4177058) # The NIH Microbiome Project (PMCID: PMC2792171)